overlap: The overlap between calibrated C14 dates

In rice: Radiocarbon Equations

The overlap between calibrated C14 dates

Description

Calculates the amount of overlap (as percentage) between two or more calibrated radiocarbon dates. It does this by taking a sequence of calendar dates 'x' and for each calendar date find the calibrated distribution with the minimum height - this minimum height is taken as the overlap between the dates for that age. This is repeated for all 'x'. The sum of these heights is the overlap, which can reach values from 0 to 100%.

Usage

overlap(
  y,
  er = c(),
  labels = c(),
  is.F = FALSE,
  res = 1000,
  cc = 1,
  postbomb = FALSE,
  deltaR = 0,
  deltaSTD = 0,
  thiscurve = NULL,
  BCAD = FALSE,
  normal = TRUE,
  t.a = 3,
  t.b = 4,
  cc.dir = NULL,
  threshold = 0,
  xlim = c(),
  xlab = c(),
  yrby = 1,
  dist.col = rgb(0, 0, 0, 0.2),
  overlap.col = rgb(0, 0, 1, 0.4),
  overlap.border = NA,
  overlap.height = 1,
  talk = TRUE,
  visualise = TRUE,
  prob = 0.95,
  roundby = 1,
  bty = "n",
  yaxt = "n"
)

Arguments

y	The set of radiocarbon dates. Alternatively, existing distributions can be provided as a list of distributions, e.g. already-calibrated distributions or distributions derived from age-model estimates.
er	The lab errors of the radiocarbon dates
labels	Labels to be printed for the distributions (optional).
is.F	Set this to TRUE if the provided age and error are in the F14C realm.
res	The resolution to base the calculations on. Defaults to 1000 steps between the minimum and maximum cal BP (these are calculated from the total calendar age range of all calibrated distributions).
cc	Calibration curve to use. Defaults to IntCal20 (cc=1).
postbomb	Whether or not to use a postbomb curve. Required for negative radiocarbon ages.
deltaR	Age offset (e.g. for marine samples).
deltaSTD	Uncertainty of the age offset (1 standard deviation).
thiscurve	As an alternative to providing cc and/or postbomb, the data of a specific curve can be provided (3 columns: cal BP, C14 age, error).
BCAD	Which calendar scale to use. Defaults to cal BP, BCAD=FALSE.
normal	Use the normal distribution to calibrate dates (default TRUE). The alternative is to use the t model (Christen and Perez 2016).
t.a	Value a of the t distribution (defaults to 3).
t.b	Value b of the t distribution (defaults to 4).
cc.dir	Directory of the calibration curves. Defaults to where the package's files are stored (system.file), but can be set to, e.g., cc.dir="curves".
threshold	Report only values above a threshold. Defaults to threshold=1e-6.
xlim	Age limits of the x-axis. Calculated automatically by default.
xlab	Label of the calendar age, defaults to BCAD or cal BP.
yrby	Resolution in years. Defaults to by=1.
dist.col	The colour of the individual (calibrated) distributions. Defaults to semi-transparent grey. Different colours can also be provided for the individual distributions.
overlap.col	The colour of the overlap distribution.
overlap.border	The colour of the border of the overlap distribution.
overlap.height	The height of the overlap distribution.
talk	Whether or not to report a summary of the spread.
visualise	Whether or not to plot the individual distributions and the overlap.
prob	Probability range to report. Defaults to prob=0.95.
roundby	Number of decimals to report.
bty	Draw a box around a box of a certain shape. Defaults to bty="n".
yaxt	Type of y-axis. Defaults to none drawn (yaxt="n").

Value

The overlap between all calibrated probabilities as percentage, and a plot.

Examples

  y <- c(3820, 4430) # the C14 ages of a twig and a marine shell from a single layer
  er <- c(40, 40) # their lab errors
  overlap(y, er, cc=1:2, dist.col=3:4, labels=c("twig", "shell"))
  mydists <- list(caldist(130,20, cc=1), caldist(150,20, cc=0))
  overlap(mydists)

rice documentation built on June 13, 2025, 5:09 p.m.